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When you say excluded folders I assume you mean exclusions to Spotlight? You could always force Spotlight to reindex your hard drive. The easiest was is in system preferences, spotlight, then privacy. Add your entire hard drive to the exclusion list, exit to let it apply, then reverse the process. This is likely to take a while.

Personally I use terminal as I feel you can search much faster this way. You can do something like the following if you say want to find a work document titled "presentation" but arent sure whether its a pages or word doc.

find ~ -name "presentation*"

this says to look in your user home folder, name is self explanatory, and the * after presentation means match any characters to account for not knowing the file type. You could search the whole drive by changing ~ to /, or add -type f after the path you are searching in if you want to only find files, as without this you are matching directories with the word presentation in the beginning.
 
Are you using 10.10 or 10.11 by any change?

In my experience Spotlight is buggy in both of them and I have similar experiences with lack of search results. Sometimes doing Spotlight reindex helps as BLUEDOG314 wrote but unfortunately issue happens again later so I am fairly certain Apple hasn't fixed the issue in 10.10 or 10.11 and I have reported it several times without success. Even deleting index in Terminal doesn't help...

Mavericks 10.9.5 doesn't have this problem in my experience.

Maybe Apple fixes it in further 10.11 update but I'm not holding my breath...

You could use EasyFind made by DevonTechnologies as a substitute...
 
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